chr2-190057123-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_005259.3(MSTN):c.*135G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00499 in 862,534 control chromosomes in the GnomAD database, including 131 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.019 ( 94 hom., cov: 32)
Exomes 𝑓: 0.0020 ( 37 hom. )
Consequence
MSTN
NM_005259.3 3_prime_UTR
NM_005259.3 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.242
Genes affected
MSTN (HGNC:4223): (myostatin) This gene encodes a secreted ligand of the TGF-beta (transforming growth factor-beta) superfamily of proteins. Ligands of this family bind various TGF-beta receptors leading to recruitment and activation of SMAD family transcription factors that regulate gene expression. The encoded preproprotein is proteolytically processed to generate each subunit of the disulfide-linked homodimer. This protein negatively regulates skeletal muscle cell proliferation and differentiation. Mutations in this gene are associated with increased skeletal muscle mass in humans and other mammals. [provided by RefSeq, Jul 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.56).
BP6
?
Variant 2-190057123-C-T is Benign according to our data. Variant chr2-190057123-C-T is described in ClinVar as [Benign]. Clinvar id is 333231.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.063 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MSTN | NM_005259.3 | c.*135G>A | 3_prime_UTR_variant | 3/3 | ENST00000260950.5 | ||
C2orf88 | XM_047446008.1 | c.-517-22831C>T | intron_variant | ||||
C2orf88 | XM_047446009.1 | c.-517-22831C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MSTN | ENST00000260950.5 | c.*135G>A | 3_prime_UTR_variant | 3/3 | 1 | NM_005259.3 | P1 | ||
C2orf88 | ENST00000478197.1 | n.220-22100C>T | intron_variant, non_coding_transcript_variant | 4 | |||||
C2orf88 | ENST00000495546.1 | n.202-22831C>T | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0187 AC: 2847AN: 151964Hom.: 94 Cov.: 32
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GnomAD4 exome AF: 0.00204 AC: 1452AN: 710452Hom.: 37 Cov.: 9 AF XY: 0.00173 AC XY: 637AN XY: 367456
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GnomAD4 genome ? AF: 0.0187 AC: 2849AN: 152082Hom.: 94 Cov.: 32 AF XY: 0.0179 AC XY: 1330AN XY: 74346
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Myostatin-related muscle hypertrophy Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 27, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign. - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at